melting analysis
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2022 ◽  
Vol 149 ◽  
pp. 107831
Author(s):  
Wenjie Wang ◽  
Zhenghua Li ◽  
Tingting Zhang ◽  
Shuangquan Hua ◽  
Shaoding Liu

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1466
Author(s):  
Maslin Osathanunkul ◽  
Panagiotis Madesis

The loss of forests is a major environmental, social, and economic problem. The disappearance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropical forests in Thailand. Floristic inventory could provide essential information for forest conservation but species identification as a part of inventory creating could be challenging in some cases. Barcode DNA coupled with High Resolution Melting analysis (Bar-HRM) was used here in aiding species identification of plant in Dipterocarpaceae (Dipterocarpus alatus, D. costatu, D. intricatus, D. obtusifolius, Hopea ferrea, H. odorata, Shorea guiso, S. obtuse, S. roxburghii, and S. siamensis) and Fagaceae (Castanopsis echinocarpa, C. inermis, Lithocarpus wallichianus, Quercus aliena and Q. oidocarpa) families. Two main experiments were conducted including: (1) a comparing method for primer design and (2) testing the robustness of the Bar-HRM by trying to identify tree samples that did not have sequences in the GenBank. In experiment 1, the manual design primer pair was found to be the best fit for the work. Of key importance is finding the primers which give the most nucleotide variations within the generated amplicon; this is a parameter that cannot be set in any web-based tools. Next, in experiment 2, Bar-HRM using primers of ITS1 and ITS2 regions were able to discriminate all 10 tested tree species without any problem, even when there were no sequences of the samples to be analysed before performing the HRM. Here, Bar-HRM poses potential to be a game-changer in tropical forest conservation, as it will be useful for species identification.


Genetica ◽  
2021 ◽  
Author(s):  
Leonardo P. Porrini ◽  
Constanza Brasesco ◽  
Matias Maggi ◽  
Martín J. Eguaras ◽  
Silvina Quintana

2021 ◽  
Vol 20 (1) ◽  
pp. 41-48
Author(s):  
Anocha Poommouang ◽  
◽  
Piyamat Kongtueng ◽  
Raksiri Nomsiri ◽  
◽  
...  

Species identification is essential and necessary in the forensic sciences. This case study aims to identify animal species using unidentified bone samples found in snake feces with the use of inter-simple sequence repeat markers coupled with high resolution melting analysis (ISSR-HRM). In this case study, six ISSR primers were used and compared with lemur blood. The results of this study indicate that the derivative melting curve established from two bones and the lemur blood sample displayed a similar melting temperature. Additionally, D-loop sequencing of the bones and blood samples were checked against the GenBank database. We found that the samples belonged to a black-and-white ruffed lemur (Varecia variegata) with percent identity values of 99.54 and 99.85, respectively. Thus, ISSR-HRM has been effectively used for species identification, particularly when results can be compared with the target species.


2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Maryam Fekri Soofi Abadi ◽  
Alireza Moradabadi ◽  
Reza Vahidi ◽  
Saeedeh Shojaeepour ◽  
Sara Rostami ◽  
...  

Abstract Background Pentavalent antimonial compounds are currently used to treat leishmaniasis and resistance to these drugs is a serious problem. Multidrug resistance protein is an efflux pump of the cell membrane that expels foreign compounds. This study designed to evaluate the mutations in the multi-drug resistance 1 (MDR1) gene, in biopsy specimens of Leishmania tropica, with high resolution melting (HRM) method. In this experimental study, genomic DNA was extracted from 130 patients with skin leishmaniasis. Then, nucleotide changes were investigated throughout the gene using HRM and sequencing methods. The samples categorized in 5 groups by differences in the melting temperature (Tm). Result The nucleotide changes analysis showed that 61% of the samples of different groups that were unresponsive to drug had mutations in the MDR1 gene, which were also confirmed by the sequencing method. These mutations can be one of the factors responsible for non-responsiveness to the treatment. Conclusion According to the findings, it seems that mutation in MDR1 gene could be responsible for drug resistance to pentavalent antimonial compounds. Furthermore, HRM method can be used to diagnose drug resistance in leishmaniasis. It is also recommended that further studies be done regarding the importance of drug resistance in the leishmania affected patients.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tomasz Olesiński ◽  
Anna Lutkowska ◽  
Adam Balcerek ◽  
Anna Sowińska ◽  
P Piotrowski ◽  
...  

AbstractThe role of the long noncoding RNA CCAT1 NC_000008.10:g.128220661C > T (rs67085638) in the development of colon cancer has been reported. Therefore, we assessed the prevalence of rs67085638 in patients with gastric cancer (GC). We also evaluated the effect of rs67085638 on B-cell-specific Moloney leukaemia virus insertion site 1 (BMI1) transcripts in primary GC and counterpart histopathologically confirmed disease-free margin tissue. Using high-resolution melting analysis, we evaluated rs67085638 frequency in patients with the GC genotype (n = 214) and controls (n = 502) in a Polish Caucasian population. qRT-PCR was used to determine BMI1 transcripts. We observed the trend of rs67085638 association in all patients with GC (ptrend = 0.028), a strong risk of the GC genotype in male (ptrend = 0.035) but not female (ptrend = 0.747) patients, and the association with non-cardia GC (ptrend = 0.041), tumour stages T3 (ptrend = 0.014) and T4 (ptrend = 0.032), differentiation grading G3 (ptrend = 0.009), lymph node metastasis stage N3 (ptrend = 0.0005) and metastasis stage M0 (ptrend = 0.027). We found that significantly increased BMI1 transcripts were associated with the primary GC genotype classified as grade G3 (p = 0.011) and as lymph node metastasis N3 (p = 0.010) and counterpart marginal tissues (p = 0.026, p = 0.040, respectively) from carriers of the T/T versus C/C genotypes. rs67085638 may contribute to increased BMI1 transcripts and the progression and rapid growth of GC.


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